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- PDB-6rcd: Octamer C-Domain P140 Mycoplasma genitalium. -

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Basic information

Entry
Database: PDB / ID: 6rcd
TitleOctamer C-Domain P140 Mycoplasma genitalium.
ComponentsMgPa adhesin
KeywordsCELL ADHESION / Domain-refolding / octamer
Function / homology
Function and homology information


adhesion of symbiont to microvasculature / membrane => GO:0016020 / plasma membrane
Similarity search - Function
Adhesin P1, C-terminal domain / Adhesin P1, N-terminal / Adhesin P1 / Mycoplasma adhesin P1, C-terminal / Mycoplasma adhesin P1, N-terminal
Similarity search - Domain/homology
MgPa adhesin / Adhesin P1
Similarity search - Component
Biological speciesMycoplasma genitalium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.98 Å
AuthorsVizarraga, D. / Aparicio, D. / Perez, R. / Illanes, R. / Fita, I.
Funding support Spain, 1items
OrganizationGrant numberCountry
Spanish Ministry of Economy and Competitiveness Spain
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2020
Title: Alternative conformation of the C-domain of the P140 protein from Mycoplasma genitalium.
Authors: Vizarraga, D. / Perez-Luque, R. / Martin, J. / Fita, I. / Aparicio, D.
History
DepositionApr 11, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 4, 2020Provider: repository / Type: Initial release
Revision 1.1Nov 18, 2020Group: Database references / Structure summary / Category: citation / struct
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _struct.title
Revision 1.2Jan 24, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / refine
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _refine.pdbx_diffrn_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: MgPa adhesin
B: MgPa adhesin
C: MgPa adhesin
D: MgPa adhesin
E: MgPa adhesin
F: MgPa adhesin
G: MgPa adhesin
X: MgPa adhesin


Theoretical massNumber of molelcules
Total (without water)92,2888
Polymers92,2888
Non-polymers00
Water10,593588
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: The octamer forms into the conditions of the hanging drop.
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area26550 Å2
ΔGint-122 kcal/mol
Surface area35310 Å2
MethodPISA
Unit cell
Length a, b, c (Å)114.509, 83.020, 118.160
Angle α, β, γ (deg.)90.00, 117.50, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11C-224-

HOH

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Components

#1: Protein
MgPa adhesin


Mass: 11535.963 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycoplasma genitalium (bacteria) / Gene: mgpB, MG191 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: D5FY31, UniProt: P20796*PLUS
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 588 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.7 Å3/Da / Density % sol: 54.43 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: DL-Malic acid and Bis-Tris propane

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 1.07216 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 27, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.07216 Å / Relative weight: 1
ReflectionResolution: 1.98→52.41 Å / Num. obs: 67417 / % possible obs: 98.5 % / Redundancy: 3.4 % / Biso Wilson estimate: 38.38 Å2 / CC1/2: 0.998 / Net I/σ(I): 10.5
Reflection shellResolution: 1.98→2.09 Å / Num. unique obs: 9766

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Processing

Software
NameVersionClassification
BUSTER2.10.3refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6RCC

6rcc


Resolution: 1.98→52.41 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.944 / SU R Cruickshank DPI: 0.147 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.15 / SU Rfree Blow DPI: 0.132 / SU Rfree Cruickshank DPI: 0.132
RfactorNum. reflection% reflectionSelection details
Rfree0.206 3390 5.03 %RANDOM
Rwork0.176 ---
obs0.178 67416 98.3 %-
Displacement parametersBiso mean: 46.22 Å2
Baniso -1Baniso -2Baniso -3
1--0.7828 Å20 Å21.6893 Å2
2---5.8972 Å20 Å2
3---6.68 Å2
Refine analyzeLuzzati coordinate error obs: 0.23 Å
Refinement stepCycle: LAST / Resolution: 1.98→52.41 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6377 0 0 588 6965
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.016553HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.048942HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d2152SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes1106HARMONIC5
X-RAY DIFFRACTIONt_it6553HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion3.49
X-RAY DIFFRACTIONt_other_torsion17.44
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion843SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact7663SEMIHARMONIC4
LS refinement shellResolution: 1.98→1.99 Å / Total num. of bins used: 50
RfactorNum. reflection% reflection
Rfree0.2724 -4.82 %
Rwork0.22 1284 -
all0.2226 1349 -
obs--97.16 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.85470.32620.07411.51680.01911.4318-0.0231-0.06590.14930.06660.06560.0425-0.2722-0.0421-0.0425-0.0340.00710.0292-0.0269-0.0203-0.0673-28.969716.629734.1177
20.49410.99090.2151.56390.84461.4064-0.03720.0339-0.10920.16470.062-0.09130.17720.0612-0.02480.00260.0053-0.0224-0.075-0.0227-0.022-22.0369-7.82458.8904
30.7632-0.528-0.19540.9032-0.90752.89710.0309-0.05040.11340.0938-0.0653-0.0866-0.38150.49130.0344-0.0857-0.08880.00040.01620.0099-0.06781.117312.122417.5563
41.3944-0.58220.67060.5755-0.81621.9310.0384-0.12240.12770.0747-0.1084-0.045-0.16980.24210.0699-0.0055-0.09390.0009-0.0055-0.0548-0.0789-7.962413.749642.8812
52.1033-0.8734-0.11081.2473-0.14621.29260.1380.115-0.11810.0207-0.14990.14230.0893-0.11860.0119-0.0616-0.04380.0058-0.0141-0.0166-0.0745-32.738-5.958933.0697
61.18220.3734-0.48670.6907-0.21351.2765-0.0677-0.1284-0.20760.0329-0.0267-0.03640.14620.20110.0944-0.03290.0172-0.0001-0.00770.0202-0.053-11.8601-8.850643.032
72.56740.685-0.3910.7035-0.08651.48140.0672-0.1569-0.2409-0.0475-0.1441-0.18770.19560.38320.0769-0.07940.0546-0.0049-0.00360.0252-0.0704-0.9659-10.505319.0302
81.4078-0.19850.10160.6266-0.31621.42890.14870.02310.0084-0.0555-0.0918-0.02150.02-0.0144-0.05690.00960.01150.011-0.09240.0246-0.0252-19.72614.49478.7958
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ A|* }
2X-RAY DIFFRACTION2{ B|* }
3X-RAY DIFFRACTION3{ C|* }
4X-RAY DIFFRACTION4{ D|* }
5X-RAY DIFFRACTION5{ E|* }
6X-RAY DIFFRACTION6{ F|* }
7X-RAY DIFFRACTION7{ G|* }
8X-RAY DIFFRACTION8{ X|* }

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